Abstract
Cancer can develop from an accumulation of alterations, some of which cause a nonmalignant cell to transform to a malignant state exhibiting increased rate of cell growth and evasion of growth suppressive mechanisms, eventually leading to tissue invasion and metastatic disease. Triple-negative breast cancers (TNBC) are heterogeneous and are clinically characterized by the lack of expression of hormone receptors and human epidermal growth factor receptor 2 (HER2), which limits its treatment options. Since tumor evolution is driven by diverse cancer cell populations and their microenvironment, it is imperative to map TNBC at single-cell resolution. Here, we describe an experimental procedure for isolating a single-cell suspension from a TNBC patient-derived xenograft, subjecting it to single-cell RNA sequencing using droplet-based technology from 10× Genomics and analyzing the transcriptomic data at single-cell resolution to obtain inferred copy number aberration profiles, using scCNA. Data obtained using this single-cell RNA sequencing experimental and analytical methodology should enhance our understanding of intratumor heterogeneity which is key for identifying genetic vulnerabilities and developing effective therapies.
Key words
- Copy number aberration
- Single-cell RNA sequencing
- Inferred copy number
- Triple-negative breast cancer
- Genomics
- Cancer heterogeneity
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Acknowledgments
The scRNAseq protocol was developed for and tested at the “Wellcome Trust Advanced Course in RNA transcriptomics.”
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Kuzmin, E. et al. (2021). Inferring Copy Number from Triple-Negative Breast Cancer Patient Derived Xenograft scRNAseq Data Using scCNA. In: Vizeacoumar, F.J., Freywald, A. (eds) Mapping Genetic Interactions. Methods in Molecular Biology, vol 2381. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1740-3_16
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DOI: https://doi.org/10.1007/978-1-0716-1740-3_16
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